Starting phenix.real_space_refine on Wed Aug 5 13:15:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ziy_74288/08_2026/9ziy_74288.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ziy_74288/08_2026/9ziy_74288.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ziy_74288/08_2026/9ziy_74288.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ziy_74288/08_2026/9ziy_74288.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ziy_74288/08_2026/9ziy_74288.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ziy_74288/08_2026/9ziy_74288.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 417 5.49 5 Mg 21 5.21 5 S 3 5.16 5 C 4604 2.51 5 N 1835 2.21 5 O 3050 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9930 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 8962 Classifications: {'RNA': 417} Modifications used: {'rna2p_pur': 28, 'rna2p_pyr': 20, 'rna3p_pur': 215, 'rna3p_pyr': 154} Link IDs: {'rna2p': 48, 'rna3p': 368} Chain: "B" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 947 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Unusual residues: {' MG': 21} Classifications: {'undetermined': 21} Link IDs: {None: 20} Time building chain proxies: 2.07, per 1000 atoms: 0.21 Number of scatterers: 9930 At special positions: 0 Unit cell: (91.5, 167.75, 151.738, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 3 16.00 P 417 15.00 Mg 21 11.99 O 3050 8.00 N 1835 7.00 C 4604 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 48.4 milliseconds 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 216 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 1 sheets defined 47.4% alpha, 14.7% beta 131 base pairs and 202 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'B' and resid 10 through 20 Processing helix chain 'B' and resid 48 through 52 removed outlier: 3.585A pdb=" N GLY B 52 " --> pdb=" O LYS B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 71 Processing helix chain 'B' and resid 87 through 90 Processing helix chain 'B' and resid 93 through 108 Processing sheet with id=AA1, first strand: chain 'B' and resid 21 through 24 removed outlier: 3.570A pdb=" N LEU B 33 " --> pdb=" O ASP B 80 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP B 80 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE B 83 " --> pdb=" O GLY B 44 " (cutoff:3.500A) 45 hydrogen bonds defined for protein. 126 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 335 hydrogen bonds 558 hydrogen bond angles 0 basepair planarities 131 basepair parallelities 202 stacking parallelities Total time for adding SS restraints: 2.33 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1032 1.33 - 1.45: 5280 1.45 - 1.57: 3850 1.57 - 1.68: 833 1.68 - 1.80: 5 Bond restraints: 11000 Sorted by residual: bond pdb=" N9 A A 261 " pdb=" C4 A A 261 " ideal model delta sigma weight residual 1.374 1.357 0.017 6.00e-03 2.78e+04 7.91e+00 bond pdb=" C2 G A 32 " pdb=" N3 G A 32 " ideal model delta sigma weight residual 1.323 1.301 0.022 8.00e-03 1.56e+04 7.52e+00 bond pdb=" C4 C A 207 " pdb=" N4 C A 207 " ideal model delta sigma weight residual 1.335 1.316 0.019 9.00e-03 1.23e+04 4.59e+00 bond pdb=" N9 A A 205 " pdb=" C4 A A 205 " ideal model delta sigma weight residual 1.374 1.386 -0.012 6.00e-03 2.78e+04 4.00e+00 bond pdb=" N9 G A 31 " pdb=" C4 G A 31 " ideal model delta sigma weight residual 1.375 1.391 -0.016 8.00e-03 1.56e+04 3.98e+00 ... (remaining 10995 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 15813 2.05 - 4.09: 1102 4.09 - 6.14: 27 6.14 - 8.18: 1 8.18 - 10.23: 1 Bond angle restraints: 16944 Sorted by residual: angle pdb=" N3 C A 207 " pdb=" C4 C A 207 " pdb=" N4 C A 207 " ideal model delta sigma weight residual 118.00 112.90 5.10 7.00e-01 2.04e+00 5.31e+01 angle pdb=" O2 C A 36 " pdb=" C2 C A 36 " pdb=" N3 C A 36 " ideal model delta sigma weight residual 121.90 116.94 4.96 7.00e-01 2.04e+00 5.03e+01 angle pdb=" O2 C A 183 " pdb=" C2 C A 183 " pdb=" N3 C A 183 " ideal model delta sigma weight residual 121.90 117.81 4.09 7.00e-01 2.04e+00 3.42e+01 angle pdb=" C1' C A 245 " pdb=" N1 C A 245 " pdb=" C2 C A 245 " ideal model delta sigma weight residual 118.80 124.88 -6.08 1.10e+00 8.26e-01 3.06e+01 angle pdb=" N3 C A 207 " pdb=" C4 C A 207 " pdb=" C5 C A 207 " ideal model delta sigma weight residual 121.90 124.06 -2.16 4.00e-01 6.25e+00 2.91e+01 ... (remaining 16939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.48: 5833 32.48 - 64.97: 1125 64.97 - 97.45: 151 97.45 - 129.94: 5 129.94 - 162.42: 2 Dihedral angle restraints: 7116 sinusoidal: 6779 harmonic: 337 Sorted by residual: dihedral pdb=" O4' U A 180 " pdb=" C1' U A 180 " pdb=" N1 U A 180 " pdb=" C2 U A 180 " ideal model delta sinusoidal sigma weight residual -160.00 -34.52 -125.48 1 1.50e+01 4.44e-03 6.74e+01 dihedral pdb=" O4' C A 318 " pdb=" C1' C A 318 " pdb=" N1 C A 318 " pdb=" C2 C A 318 " ideal model delta sinusoidal sigma weight residual -160.00 -99.24 -60.76 1 1.50e+01 4.44e-03 2.18e+01 dihedral pdb=" O4' G A 213 " pdb=" C1' G A 213 " pdb=" N9 G A 213 " pdb=" C4 G A 213 " ideal model delta sinusoidal sigma weight residual -106.00 -166.19 60.19 1 1.70e+01 3.46e-03 1.67e+01 ... (remaining 7113 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1568 0.045 - 0.090: 232 0.090 - 0.136: 325 0.136 - 0.181: 92 0.181 - 0.226: 4 Chirality restraints: 2221 Sorted by residual: chirality pdb=" C3' A A 148 " pdb=" C4' A A 148 " pdb=" O3' A A 148 " pdb=" C2' A A 148 " both_signs ideal model delta sigma weight residual False -2.48 -2.25 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" C1' A A 50 " pdb=" O4' A A 50 " pdb=" C2' A A 50 " pdb=" N9 A A 50 " both_signs ideal model delta sigma weight residual False 2.47 2.25 0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" C1' A A 187 " pdb=" O4' A A 187 " pdb=" C2' A A 187 " pdb=" N9 A A 187 " both_signs ideal model delta sigma weight residual False 2.47 2.28 0.19 2.00e-01 2.50e+01 9.47e-01 ... (remaining 2218 not shown) Planarity restraints: 581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G A 32 " 0.008 2.00e-02 2.50e+03 1.76e-02 9.31e+00 pdb=" N9 G A 32 " -0.010 2.00e-02 2.50e+03 pdb=" C8 G A 32 " -0.001 2.00e-02 2.50e+03 pdb=" N7 G A 32 " -0.006 2.00e-02 2.50e+03 pdb=" C5 G A 32 " -0.003 2.00e-02 2.50e+03 pdb=" C6 G A 32 " 0.013 2.00e-02 2.50e+03 pdb=" O6 G A 32 " -0.003 2.00e-02 2.50e+03 pdb=" N1 G A 32 " -0.008 2.00e-02 2.50e+03 pdb=" C2 G A 32 " 0.049 2.00e-02 2.50e+03 pdb=" N2 G A 32 " -0.030 2.00e-02 2.50e+03 pdb=" N3 G A 32 " -0.005 2.00e-02 2.50e+03 pdb=" C4 G A 32 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A 36 " 0.008 2.00e-02 2.50e+03 1.69e-02 6.41e+00 pdb=" N1 C A 36 " -0.003 2.00e-02 2.50e+03 pdb=" C2 C A 36 " -0.042 2.00e-02 2.50e+03 pdb=" O2 C A 36 " 0.021 2.00e-02 2.50e+03 pdb=" N3 C A 36 " 0.008 2.00e-02 2.50e+03 pdb=" C4 C A 36 " -0.009 2.00e-02 2.50e+03 pdb=" N4 C A 36 " 0.009 2.00e-02 2.50e+03 pdb=" C5 C A 36 " 0.003 2.00e-02 2.50e+03 pdb=" C6 C A 36 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C A 183 " 0.022 2.00e-02 2.50e+03 1.68e-02 6.33e+00 pdb=" N1 C A 183 " -0.029 2.00e-02 2.50e+03 pdb=" C2 C A 183 " 0.022 2.00e-02 2.50e+03 pdb=" O2 C A 183 " -0.012 2.00e-02 2.50e+03 pdb=" N3 C A 183 " -0.011 2.00e-02 2.50e+03 pdb=" C4 C A 183 " 0.019 2.00e-02 2.50e+03 pdb=" N4 C A 183 " -0.001 2.00e-02 2.50e+03 pdb=" C5 C A 183 " -0.001 2.00e-02 2.50e+03 pdb=" C6 C A 183 " -0.010 2.00e-02 2.50e+03 ... (remaining 578 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 39 2.50 - 3.10: 6652 3.10 - 3.70: 20833 3.70 - 4.30: 27846 4.30 - 4.90: 35622 Nonbonded interactions: 90992 Sorted by model distance: nonbonded pdb=" OP1 A A 257 " pdb="MG MG A 506 " model vdw 1.896 2.170 nonbonded pdb=" OP2 C A 278 " pdb="MG MG A 508 " model vdw 1.929 2.170 nonbonded pdb=" OP1 G A 275 " pdb="MG MG A 509 " model vdw 1.961 2.170 nonbonded pdb=" O6 G A 299 " pdb="MG MG A 513 " model vdw 1.964 2.170 nonbonded pdb=" O2' A A 277 " pdb="MG MG A 508 " model vdw 1.968 2.170 ... (remaining 90987 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 10.380 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11000 Z= 0.279 Angle : 0.840 10.228 16944 Z= 0.721 Chirality : 0.063 0.226 2221 Planarity : 0.004 0.029 581 Dihedral : 25.648 162.419 6900 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 6.06 % Allowed : 37.37 % Favored : 56.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.79), residues: 114 helix: 2.30 (0.71), residues: 47 sheet: -0.04 (1.13), residues: 24 loop : -2.44 (0.82), residues: 43 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 26 TYR 0.019 0.002 TYR B 40 PHE 0.006 0.001 PHE B 13 HIS 0.000 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.28 (11000) covalent geometry : angle 0.83992 / 0.72 (16944) hydrogen bonds : bond 0.09759 / 10.79 ( 380) hydrogen bonds : angle 3.12146 / 4.10 ( 684) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.183 Fit side-chains REVERT: B 35 ARG cc_start: 0.8123 (mmt90) cc_final: 0.7798 (tpp80) REVERT: B 70 GLU cc_start: 0.8838 (tm-30) cc_final: 0.8143 (tm-30) REVERT: B 113 LYS cc_start: 0.8170 (tptm) cc_final: 0.7571 (tptp) outliers start: 6 outliers final: 4 residues processed: 33 average time/residue: 0.1097 time to fit residues: 5.1124 Evaluate side-chains 34 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 10.0000 chunk 48 optimal weight: 0.0010 chunk 26 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 16 optimal weight: 50.0000 chunk 32 optimal weight: 8.9990 chunk 31 optimal weight: 20.0000 chunk 25 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 20.0000 chunk 30 optimal weight: 10.0000 overall best weight: 6.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.068750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.041126 restraints weight = 70446.516| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 2.23 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 11000 Z= 0.409 Angle : 0.881 9.666 16944 Z= 0.457 Chirality : 0.060 0.299 2221 Planarity : 0.007 0.036 581 Dihedral : 25.898 171.025 6654 Min Nonbonded Distance : 1.599 Molprobity Statistics. All-atom Clashscore : 34.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 9.09 % Allowed : 35.35 % Favored : 55.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.80), residues: 114 helix: 1.46 (0.67), residues: 47 sheet: -1.13 (0.97), residues: 26 loop : -2.38 (1.08), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 65 TYR 0.014 0.002 TYR B 40 PHE 0.028 0.004 PHE B 13 HIS 0.003 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00630 / 0.41 (11000) covalent geometry : angle 0.88125 / 0.46 (16944) hydrogen bonds : bond 0.13931 / 14.52 ( 380) hydrogen bonds : angle 3.11000 / 4.28 ( 684) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 28 time to evaluate : 0.156 Fit side-chains REVERT: B 35 ARG cc_start: 0.8066 (mmt90) cc_final: 0.7816 (tpp80) REVERT: B 70 GLU cc_start: 0.8807 (tm-30) cc_final: 0.8206 (tm-30) REVERT: B 113 LYS cc_start: 0.8277 (tptm) cc_final: 0.7733 (tptp) outliers start: 9 outliers final: 7 residues processed: 33 average time/residue: 0.1053 time to fit residues: 4.9016 Evaluate side-chains 34 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 71 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 33 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 37 optimal weight: 20.0000 chunk 41 optimal weight: 0.0770 chunk 35 optimal weight: 30.0000 chunk 28 optimal weight: 10.0000 chunk 14 optimal weight: 30.0000 chunk 26 optimal weight: 20.0000 chunk 30 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 overall best weight: 7.2148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.067307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.039464 restraints weight = 73438.047| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 2.18 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 11000 Z= 0.442 Angle : 0.941 12.373 16944 Z= 0.487 Chirality : 0.064 0.582 2221 Planarity : 0.007 0.026 581 Dihedral : 26.503 177.077 6650 Min Nonbonded Distance : 1.620 Molprobity Statistics. All-atom Clashscore : 38.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 13.13 % Allowed : 32.32 % Favored : 54.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.81), residues: 114 helix: 0.74 (0.67), residues: 47 sheet: -1.80 (0.95), residues: 25 loop : -2.39 (1.14), residues: 42 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 26 TYR 0.017 0.003 TYR B 5 PHE 0.029 0.004 PHE B 13 HIS 0.005 0.003 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00683 / 0.44 (11000) covalent geometry : angle 0.94130 / 0.49 (16944) hydrogen bonds : bond 0.15298 / 15.84 ( 380) hydrogen bonds : angle 3.26574 / 4.62 ( 684) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 29 time to evaluate : 0.096 Fit side-chains REVERT: B 35 ARG cc_start: 0.8236 (mmt90) cc_final: 0.7979 (tpp80) REVERT: B 43 ILE cc_start: 0.8623 (OUTLIER) cc_final: 0.8340 (pt) REVERT: B 68 PHE cc_start: 0.9184 (OUTLIER) cc_final: 0.8242 (t80) REVERT: B 70 GLU cc_start: 0.8797 (tm-30) cc_final: 0.8167 (tm-30) REVERT: B 113 LYS cc_start: 0.8232 (tptm) cc_final: 0.7567 (tptp) outliers start: 13 outliers final: 8 residues processed: 37 average time/residue: 0.0955 time to fit residues: 4.9454 Evaluate side-chains 39 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 29 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 97 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 0 optimal weight: 20.0000 chunk 8 optimal weight: 10.0000 chunk 50 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 37 optimal weight: 20.0000 chunk 4 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 17 optimal weight: 40.0000 chunk 18 optimal weight: 20.0000 chunk 9 optimal weight: 10.0000 chunk 31 optimal weight: 20.0000 overall best weight: 6.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.067278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.039636 restraints weight = 73867.319| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 1.92 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 11000 Z= 0.394 Angle : 0.868 12.449 16944 Z= 0.455 Chirality : 0.059 0.330 2221 Planarity : 0.006 0.049 581 Dihedral : 26.447 179.082 6647 Min Nonbonded Distance : 1.631 Molprobity Statistics. All-atom Clashscore : 36.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.16 % Favored : 86.84 % Rotamer: Outliers : 12.12 % Allowed : 31.31 % Favored : 56.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.83), residues: 114 helix: 0.96 (0.68), residues: 47 sheet: -1.60 (1.04), residues: 26 loop : -2.42 (1.16), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG B 86 TYR 0.012 0.003 TYR B 5 PHE 0.027 0.003 PHE B 13 HIS 0.004 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00611 / 0.39 (11000) covalent geometry : angle 0.86808 / 0.45 (16944) hydrogen bonds : bond 0.14500 / 14.98 ( 380) hydrogen bonds : angle 3.18434 / 4.46 ( 684) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 29 time to evaluate : 0.144 Fit side-chains REVERT: B 35 ARG cc_start: 0.8149 (mmt90) cc_final: 0.7865 (tpp80) REVERT: B 68 PHE cc_start: 0.9148 (OUTLIER) cc_final: 0.8248 (t80) REVERT: B 70 GLU cc_start: 0.8808 (tm-30) cc_final: 0.8136 (tm-30) REVERT: B 113 LYS cc_start: 0.8345 (tptm) cc_final: 0.7708 (tptp) outliers start: 12 outliers final: 7 residues processed: 36 average time/residue: 0.1005 time to fit residues: 5.0505 Evaluate side-chains 36 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 46 optimal weight: 0.4980 chunk 30 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 26 optimal weight: 20.0000 chunk 11 optimal weight: 10.0000 chunk 18 optimal weight: 20.0000 chunk 13 optimal weight: 20.0000 chunk 3 optimal weight: 20.0000 chunk 47 optimal weight: 0.6980 chunk 20 optimal weight: 50.0000 overall best weight: 4.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.067799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.040620 restraints weight = 73002.464| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 1.72 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 11000 Z= 0.296 Angle : 0.728 12.319 16944 Z= 0.398 Chirality : 0.050 0.317 2221 Planarity : 0.005 0.025 581 Dihedral : 26.425 176.787 6647 Min Nonbonded Distance : 1.688 Molprobity Statistics. All-atom Clashscore : 30.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.40 % Favored : 88.60 % Rotamer: Outliers : 10.10 % Allowed : 30.30 % Favored : 59.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.85), residues: 114 helix: 1.26 (0.72), residues: 47 sheet: -1.85 (0.96), residues: 26 loop : -2.21 (1.20), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 86 TYR 0.009 0.002 TYR B 5 PHE 0.019 0.003 PHE B 13 HIS 0.003 0.002 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.30 (11000) covalent geometry : angle 0.72770 / 0.40 (16944) hydrogen bonds : bond 0.12330 / 12.82 ( 380) hydrogen bonds : angle 2.95644 / 4.14 ( 684) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 29 time to evaluate : 0.138 Fit side-chains REVERT: B 35 ARG cc_start: 0.8217 (mmt90) cc_final: 0.7834 (tpp80) REVERT: B 68 PHE cc_start: 0.9148 (OUTLIER) cc_final: 0.8164 (t80) REVERT: B 70 GLU cc_start: 0.8782 (tm-30) cc_final: 0.8147 (tm-30) REVERT: B 113 LYS cc_start: 0.8353 (tptm) cc_final: 0.7749 (tptp) outliers start: 10 outliers final: 7 residues processed: 34 average time/residue: 0.0999 time to fit residues: 4.8145 Evaluate side-chains 37 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 27 optimal weight: 10.0000 chunk 22 optimal weight: 50.0000 chunk 29 optimal weight: 9.9990 chunk 20 optimal weight: 50.0000 chunk 11 optimal weight: 20.0000 chunk 21 optimal weight: 50.0000 chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 chunk 37 optimal weight: 20.0000 chunk 9 optimal weight: 10.0000 chunk 35 optimal weight: 30.0000 overall best weight: 8.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.066045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.038398 restraints weight = 76409.119| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 2.69 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.086 11000 Z= 0.556 Angle : 1.104 13.593 16944 Z= 0.549 Chirality : 0.073 0.354 2221 Planarity : 0.007 0.034 581 Dihedral : 26.782 178.390 6647 Min Nonbonded Distance : 1.606 Molprobity Statistics. All-atom Clashscore : 47.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.91 % Favored : 85.09 % Rotamer: Outliers : 13.13 % Allowed : 29.29 % Favored : 57.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.84), residues: 114 helix: 0.25 (0.69), residues: 53 sheet: -1.60 (1.00), residues: 26 loop : -2.41 (1.32), residues: 35 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG B 26 TYR 0.013 0.003 TYR B 5 PHE 0.029 0.004 PHE B 13 HIS 0.005 0.003 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00856 / 0.56 (11000) covalent geometry : angle 1.10429 / 0.55 (16944) hydrogen bonds : bond 0.17314 / 17.87 ( 380) hydrogen bonds : angle 3.40965 / 4.66 ( 684) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 28 time to evaluate : 0.095 Fit side-chains REVERT: B 35 ARG cc_start: 0.8091 (mmt90) cc_final: 0.7810 (tpp80) REVERT: B 68 PHE cc_start: 0.9141 (OUTLIER) cc_final: 0.8351 (t80) REVERT: B 70 GLU cc_start: 0.8810 (tm-30) cc_final: 0.8145 (tm-30) REVERT: B 113 LYS cc_start: 0.8438 (tptm) cc_final: 0.7898 (tptp) outliers start: 13 outliers final: 9 residues processed: 35 average time/residue: 0.0804 time to fit residues: 3.9177 Evaluate side-chains 40 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 30 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 12 optimal weight: 30.0000 chunk 11 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 37 optimal weight: 20.0000 chunk 15 optimal weight: 50.0000 chunk 21 optimal weight: 50.0000 chunk 40 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 overall best weight: 7.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.065920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.038508 restraints weight = 75783.508| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 2.23 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.4565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 11000 Z= 0.456 Angle : 0.962 10.146 16944 Z= 0.495 Chirality : 0.065 0.369 2221 Planarity : 0.007 0.032 581 Dihedral : 26.951 179.701 6647 Min Nonbonded Distance : 1.609 Molprobity Statistics. All-atom Clashscore : 42.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.16 % Favored : 86.84 % Rotamer: Outliers : 12.12 % Allowed : 30.30 % Favored : 57.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.88), residues: 114 helix: 0.94 (0.73), residues: 47 sheet: -1.47 (1.02), residues: 26 loop : -2.29 (1.26), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 26 TYR 0.012 0.003 TYR B 5 PHE 0.027 0.004 PHE B 13 HIS 0.005 0.003 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00704 / 0.46 (11000) covalent geometry : angle 0.96168 / 0.50 (16944) hydrogen bonds : bond 0.15067 / 15.50 ( 380) hydrogen bonds : angle 3.22289 / 4.44 ( 684) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 28 time to evaluate : 0.145 Fit side-chains REVERT: B 18 GLN cc_start: 0.8623 (mt0) cc_final: 0.8360 (mt0) REVERT: B 68 PHE cc_start: 0.9154 (OUTLIER) cc_final: 0.8154 (t80) REVERT: B 70 GLU cc_start: 0.8799 (tm-30) cc_final: 0.8140 (tm-30) REVERT: B 96 GLU cc_start: 0.8616 (mp0) cc_final: 0.8350 (mp0) REVERT: B 113 LYS cc_start: 0.8462 (tptm) cc_final: 0.8078 (tptp) outliers start: 12 outliers final: 10 residues processed: 34 average time/residue: 0.0941 time to fit residues: 4.4610 Evaluate side-chains 37 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 26 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 15 GLU Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 31 optimal weight: 20.0000 chunk 51 optimal weight: 0.6980 chunk 7 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 23 optimal weight: 30.0000 chunk 28 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 13 optimal weight: 20.0000 chunk 6 optimal weight: 9.9990 overall best weight: 6.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.065748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.038428 restraints weight = 75813.166| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 2.32 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.4824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 11000 Z= 0.422 Angle : 0.933 9.699 16944 Z= 0.482 Chirality : 0.063 0.340 2221 Planarity : 0.006 0.041 581 Dihedral : 26.905 179.846 6647 Min Nonbonded Distance : 1.622 Molprobity Statistics. All-atom Clashscore : 43.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.54 % Favored : 82.46 % Rotamer: Outliers : 11.11 % Allowed : 29.29 % Favored : 59.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.88), residues: 114 helix: 0.98 (0.72), residues: 47 sheet: -1.58 (1.05), residues: 26 loop : -2.20 (1.25), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 26 TYR 0.010 0.003 TYR B 5 PHE 0.025 0.004 PHE B 13 HIS 0.005 0.003 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00649 / 0.42 (11000) covalent geometry : angle 0.93328 / 0.48 (16944) hydrogen bonds : bond 0.15480 / 16.03 ( 380) hydrogen bonds : angle 3.23912 / 4.39 ( 684) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 29 time to evaluate : 0.128 Fit side-chains REVERT: B 70 GLU cc_start: 0.8819 (tm-30) cc_final: 0.8119 (tm-30) REVERT: B 96 GLU cc_start: 0.8648 (mp0) cc_final: 0.8332 (mp0) REVERT: B 113 LYS cc_start: 0.8479 (tptm) cc_final: 0.8157 (tptp) outliers start: 11 outliers final: 9 residues processed: 33 average time/residue: 0.1097 time to fit residues: 5.1074 Evaluate side-chains 37 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 28 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 92 MET Chi-restraints excluded: chain B residue 111 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 2 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 31 optimal weight: 20.0000 chunk 35 optimal weight: 30.0000 chunk 40 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 14 optimal weight: 30.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.066134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.038998 restraints weight = 75117.898| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 1.86 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.4769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 11000 Z= 0.340 Angle : 0.799 8.382 16944 Z= 0.431 Chirality : 0.056 0.333 2221 Planarity : 0.006 0.023 581 Dihedral : 26.803 177.188 6647 Min Nonbonded Distance : 1.652 Molprobity Statistics. All-atom Clashscore : 35.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.04 % Favored : 85.96 % Rotamer: Outliers : 10.10 % Allowed : 31.31 % Favored : 58.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.88), residues: 114 helix: 1.16 (0.73), residues: 47 sheet: -1.35 (1.06), residues: 26 loop : -2.15 (1.26), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 26 TYR 0.008 0.002 TYR B 81 PHE 0.021 0.003 PHE B 13 HIS 0.004 0.003 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.34 (11000) covalent geometry : angle 0.79922 / 0.43 (16944) hydrogen bonds : bond 0.13472 / 13.92 ( 380) hydrogen bonds : angle 3.07314 / 4.19 ( 684) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 27 time to evaluate : 0.103 Fit side-chains REVERT: B 70 GLU cc_start: 0.8808 (tm-30) cc_final: 0.8099 (tm-30) REVERT: B 96 GLU cc_start: 0.8616 (mp0) cc_final: 0.8309 (mp0) REVERT: B 113 LYS cc_start: 0.8418 (tptm) cc_final: 0.8104 (tptp) outliers start: 10 outliers final: 8 residues processed: 32 average time/residue: 0.0785 time to fit residues: 3.6763 Evaluate side-chains 34 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 26 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 92 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 36 optimal weight: 30.0000 chunk 21 optimal weight: 50.0000 chunk 35 optimal weight: 30.0000 chunk 15 optimal weight: 50.0000 chunk 27 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 33 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.065294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.038171 restraints weight = 74655.407| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 2.45 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.5236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 11000 Z= 0.479 Angle : 1.009 11.387 16944 Z= 0.514 Chirality : 0.067 0.348 2221 Planarity : 0.007 0.030 581 Dihedral : 26.963 179.784 6647 Min Nonbonded Distance : 1.629 Molprobity Statistics. All-atom Clashscore : 47.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.30 % Favored : 80.70 % Rotamer: Outliers : 9.09 % Allowed : 31.31 % Favored : 59.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.89), residues: 114 helix: 0.92 (0.74), residues: 47 sheet: -1.44 (1.06), residues: 26 loop : -2.00 (1.28), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 86 TYR 0.016 0.003 TYR B 40 PHE 0.027 0.004 PHE B 13 HIS 0.006 0.004 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00733 / 0.48 (11000) covalent geometry : angle 1.00916 / 0.51 (16944) hydrogen bonds : bond 0.16494 / 17.02 ( 380) hydrogen bonds : angle 3.36652 / 4.54 ( 684) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 228 Ramachandran restraints generated. 114 Oldfield, 0 Emsley, 114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 27 time to evaluate : 0.089 Fit side-chains REVERT: B 70 GLU cc_start: 0.8827 (tm-30) cc_final: 0.8125 (tm-30) REVERT: B 96 GLU cc_start: 0.8612 (mp0) cc_final: 0.8278 (mp0) REVERT: B 113 LYS cc_start: 0.8501 (tptm) cc_final: 0.8209 (tptp) outliers start: 9 outliers final: 8 residues processed: 31 average time/residue: 0.0716 time to fit residues: 3.2720 Evaluate side-chains 36 residues out of total 99 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ILE Chi-restraints excluded: chain B residue 13 PHE Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 22 SER Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 84 ILE Chi-restraints excluded: chain B residue 92 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 10 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 chunk 36 optimal weight: 30.0000 chunk 7 optimal weight: 10.0000 chunk 16 optimal weight: 50.0000 chunk 19 optimal weight: 30.0000 chunk 8 optimal weight: 9.9990 chunk 46 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 33 optimal weight: 0.7980 chunk 0 optimal weight: 30.0000 overall best weight: 6.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.065534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.038154 restraints weight = 76456.479| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 2.16 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.5244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 11000 Z= 0.409 Angle : 0.899 9.502 16944 Z= 0.470 Chirality : 0.061 0.344 2221 Planarity : 0.006 0.024 581 Dihedral : 26.919 177.795 6647 Min Nonbonded Distance : 1.626 Molprobity Statistics. All-atom Clashscore : 40.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % Rotamer: Outliers : 10.10 % Allowed : 30.30 % Favored : 59.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.88), residues: 114 helix: 1.00 (0.74), residues: 47 sheet: -1.42 (1.04), residues: 26 loop : -2.08 (1.26), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 26 TYR 0.012 0.003 TYR B 40 PHE 0.024 0.004 PHE B 13 HIS 0.005 0.003 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00637 / 0.41 (11000) covalent geometry : angle 0.89874 / 0.47 (16944) hydrogen bonds : bond 0.14503 / 14.92 ( 380) hydrogen bonds : angle 3.19076 / 4.31 ( 684) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2351.25 seconds wall clock time: 41 minutes 5.36 seconds (2465.36 seconds total)